Mirau P A, Kearns D R
J Mol Biol. 1984 Aug 5;177(2):207-27. doi: 10.1016/0022-2836(84)90453-4.
High-resolution 1H nuclear magnetic resonance in H2O has been used to study the effect of sequence, conformation, environmental factors and base substituents on the exchange behavior of the hydrogen-bonded imino protons of guainine X cytosine and inosine X cytosine base-pairs in DNA, RNA, and DNA-RNA duplexes. The exchange rates were determined by measurement of the spin-lattice relaxation rates of the imino protons as a function of temperature. The exchange was not altered by the presence of high concentrations of salt, and the inability of phosphate to catalyze the exchange indicates that the exchange is limited by formation of a solvent-accessible "open" state. The exchange behavior depends on the duplex conformation and sequence. Exchange from the Z form polymers was orders of magnitude slower than the corresponding duplexes in the B conformation, and the A form RNA duplexes exchanged more slowly than the B form DNA polymers with the same sequence. The exchange behavior of the DNA-RNA hybrids was dependent on whether the purine or the pyrimidine strand contained the deoxyribose sugar. For both the guanine and inosine-containing duplexes, the homopolymer duplexes exchange more slowly than the more stable alternating copolymers. For the alternating duplexes, substitution of cytosine with 5-bromo- or 5-methylcytosine slowed the exchange and increased the activation energy for exchange. The inosine-containing duplexes exchanged more rapidly than the guanosine-containing duplexes, but both showed similar changes in exchange behavior in response to changes in sequence and base substituents. The activation energies for base-pair opening in B form DNA are correlated with the van der Waals contribution to the base-base interaction energy, suggesting that the purine base is partially unstacked in the open state. Using the relaxation measurements to set an upper limit on the exchange rate in poly(dG-dC) and the tritium exchange behavior at low temperature, we find that even though Z-DNA exchanges very slowly, the activation energy is similar to that observed in the A and B form duplexes, suggesting that exchange occurs from a similar open state.
利用水中的高分辨率¹H核磁共振技术，研究了序列、构象、环境因素和碱基取代基对DNA、RNA及DNA - RNA双链体中鸟嘌呤X胞嘧啶和肌苷X胞嘧啶碱基对的氢键亚氨基质子交换行为的影响。通过测量亚氨基质子的自旋 - 晶格弛豫速率随温度的变化来确定交换速率。高浓度盐的存在并未改变交换，且磷酸盐无法催化交换，这表明交换受形成可溶剂接触的“开放”状态的限制。交换行为取决于双链体的构象和序列。Z型聚合物的交换比B型构象的相应双链体慢几个数量级，且具有相同序列的A型RNA双链体比B型DNA聚合物交换得更慢。DNA - RNA杂交体的交换行为取决于嘌呤链还是嘧啶链含有脱氧核糖。对于含鸟嘌呤和含肌苷的双链体，均聚物双链体的交换比更稳定的交替共聚物慢。对于交替双链体，用5 - 溴胞嘧啶或5 - 甲基胞嘧啶取代胞嘧啶会减缓交换并增加交换的活化能。含肌苷的双链体比含鸟苷的双链体交换更快，但二者在序列和碱基取代基变化时均表现出相似的交换行为变化。B型DNA中碱基对打开的活化能与范德华力对碱基 - 碱基相互作用能的贡献相关联，这表明嘌呤碱基在开放状态下部分解堆叠。利用弛豫测量来设定聚（dG - dC）中交换速率的上限以及低温下的氚交换行为，我们发现尽管Z - DNA交换非常缓慢，但其活化能与A和B型双链体中观察到的相似，这表明交换是从类似的开放状态发生的。
